So, I'm guessing that if he goes sub+protect (Granted that the Palkia hasn't invested at all into speed) and if the Gligar is equipped with an Eviolite, he can easily toxic stall that space distorting dinosaur

That Gligar is going to have a hell of a time getting the Palkia toxic'd without getting his **** slapped. Even with eviolite, it's going to do a metric ******* , and without too many subs left, he's going to have a bad time, if he does survive the first move.

That taken into account, the Palkia would still **** it up good. Palkia's highest stat is Special Attack and it gets a STAB-boosted, super effective Hydro Pump.
Assuming it had no IVs or EVs and a Negative nature, Palkia's Special Attack Stat is 274.
A Gligar with maxed-out EVs and IVs and a Positive nature would have a max Defense Stat of 251
Taking into account that those are 5th Gen graphics, we'll say the Gligar has an Eviolite
We'll have the Palkia use Hydro Pump
Let's calculate the damage.
It will take away 56%-67% of Gligar's HP if the Gligar also has max HP EVs and IVs.
In two turns, the Palkia would murder the Gligar. Palkia wins.